Nevertheless, it is still a challenging bioinformatics problem to analyze and annotate the often short, redundant and yet error prone EST sequences in an appropriate and efficient manner, especially when the genome sequence of the organism is unknown. Because of recent advances in biotechnology, ESTs are produced daily in large quantities, with nearly 42 million entries in the current GenBank db EST database (release 030207). ESTs are often generated from either end of randomly selected cDNA clones and provide valuable transcriptional data for the annotation of genomic sequences. In the absence of full genome sequences, expressed sequence tags (ESTs) allow rapid identification of expressed genes by sequence analysis and are an important resource for comparative and functional genomic studies. Like many other ecologically important species, genomics research in earthworms lags far behind other model species such as Mus musculus and Caenorhabditis elegans. ![]() They have a life span of 4–5 years and are obligatorily amphimictic even though each worm has both male and female reproductive organs. andrei are two sibling species commonly found in North American composters and are sold commercially for fish bait. The earthworm species (e.g., Eisenia fetida, Eisenia andrei, and Lumbricus terrestris) widely used in standardized acute and reproduction toxicity tests belong to the Lumbricidae family (phylum, Annelida class, Clitellata subclass Oligochaeta order, Haplotaxida superfamily, Lumbricoidea family, Lumbricidae). They are increasingly recognized as indicators of agroecosystem health and ecotoxicological sentinel species because they are constantly exposed to contaminants in soil. There are over 8000 described species worldwide, existing everywhere but in Polar and arid climates. Īs key representatives of the soil fauna, earthworms are essential in maintaining soil fertility through their burrowing, ingestion and excretion activities. The ESTMD containing the sequence and annotation information of 4032 E. All the information is stored and retrievable at a highly performed, web-based and user-friendly relational database called EST model database or ESTMD version 2. Seven percent of the unique sequences were further mapped to 99 Kyoto Encyclopedia of Genes and Genomes pathways based on their matching Enzyme Commission numbers. Provisional function annotation assigned 830 Gene Ontology terms to 517 unique sequences based on their homology with the annotated genomes of four model organisms Drosophila melanogaster, Mus musculus, Saccharomyces cerevisiae, and Caenorhabditis elegans. ![]() Comparative genomic analysis showed that 743 or 33% of the unique sequences shared high similarity with existing genes in the GenBank nr database. Clustering analysis yielded 2231 unique sequences including 448 contigs (from 1361 ESTs) and 1783 singletons. ResultsĪ total of 3144 good quality ESTs (GenBank dbEST accession number EH669363–EH672369 and EL515444–EL515580) were obtained from the raw clone sequences after cleaning. fetida libraries enriched with genes responsive to ten ordnance related compounds using suppressive subtractive hybridization-PCR. In order to understand its gene expression response to environmental contaminants, we cloned 4032 cDNAs or expressed sequence tags (ESTs) from two E. Little is known about its genome sequence although it has been extensively used as a test organism in terrestrial ecotoxicology. Eisenia fetida, commonly known as red wiggler or compost worm, belongs to the Lumbricidae family of the Annelida phylum.
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